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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 4-186083063-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=186083063&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "TLR3",
"hgnc_id": 11849,
"hgvs_c": "c.1377C>T",
"hgvs_p": "p.Phe459Phe",
"inheritance_mode": "AR,AD,Unknown",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_003265.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_score": -21,
"allele_count_reference_population": 487359,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"chr": "4",
"clinvar_classification": "Benign",
"clinvar_disease": " 1, susceptibility to,Herpes simplex encephalitis,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5 O:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7300000190734863,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 904,
"aa_ref": "F",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6015,
"cdna_start": 1477,
"cds_end": null,
"cds_length": 2715,
"cds_start": 1377,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_003265.3",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.1377C>T",
"hgvs_p": "p.Phe459Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000296795.8",
"protein_coding": true,
"protein_id": "NP_003256.1",
"strand": true,
"transcript": "NM_003265.3",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 904,
"aa_ref": "F",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6015,
"cdna_start": 1477,
"cds_end": null,
"cds_length": 2715,
"cds_start": 1377,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000296795.8",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.1377C>T",
"hgvs_p": "p.Phe459Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003265.3",
"protein_coding": true,
"protein_id": "ENSP00000296795.3",
"strand": true,
"transcript": "ENST00000296795.8",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 627,
"aa_ref": "F",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2942,
"cdna_start": 1453,
"cds_end": null,
"cds_length": 1884,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000512264.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Phe182Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513668.1",
"strand": true,
"transcript": "ENST00000512264.1",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 904,
"aa_ref": "F",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4661,
"cdna_start": 1480,
"cds_end": null,
"cds_length": 2715,
"cds_start": 1377,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000949725.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.1377C>T",
"hgvs_p": "p.Phe459Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619784.1",
"strand": true,
"transcript": "ENST00000949725.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 904,
"aa_ref": "F",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3223,
"cdna_start": 1662,
"cds_end": null,
"cds_length": 2715,
"cds_start": 1377,
"consequences": [
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000949726.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.1377C>T",
"hgvs_p": "p.Phe459Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619785.1",
"strand": true,
"transcript": "ENST00000949726.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 904,
"aa_ref": "F",
"aa_start": 459,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4709,
"cdna_start": 1525,
"cds_end": null,
"cds_length": 2715,
"cds_start": 1377,
"consequences": [
"synonymous_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000949727.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.1377C>T",
"hgvs_p": "p.Phe459Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000619786.1",
"strand": true,
"transcript": "ENST00000949727.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 627,
"aa_ref": "F",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2310,
"cdna_start": 956,
"cds_end": null,
"cds_length": 1884,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000504367.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Phe182Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000423684.1",
"strand": true,
"transcript": "ENST00000504367.1",
"transcript_support_level": 2
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 627,
"aa_ref": "F",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2328,
"cdna_start": 974,
"cds_end": null,
"cds_length": 1884,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000508051.2",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Phe182Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513677.1",
"strand": true,
"transcript": "ENST00000508051.2",
"transcript_support_level": 3
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 627,
"aa_ref": "F",
"aa_start": 182,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5389,
"cdna_start": 880,
"cds_end": null,
"cds_length": 1884,
"cds_start": 546,
"consequences": [
"synonymous_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000698354.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.546C>T",
"hgvs_p": "p.Phe182Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513676.1",
"strand": true,
"transcript": "ENST00000698354.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 299,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1589,
"cdna_start": null,
"cds_end": null,
"cds_length": 900,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000698351.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "c.864+513C>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513674.1",
"strand": true,
"transcript": "ENST00000698351.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5737,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000698352.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "n.*929C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513675.1",
"strand": true,
"transcript": "ENST00000698352.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 5761,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000698353.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "n.1252C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000698353.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5737,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000698352.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "n.*929C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513675.1",
"strand": true,
"transcript": "ENST00000698352.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "non_stop_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1156,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000513189.1",
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"hgvs_c": "n.*130C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000423386.1",
"strand": true,
"transcript": "ENST00000513189.1",
"transcript_support_level": 1
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs3775290",
"effect": "synonymous_variant",
"frequency_reference_population": 0.30199468,
"gene_hgnc_id": 11849,
"gene_symbol": "TLR3",
"gnomad_exomes_ac": 445532,
"gnomad_exomes_af": 0.30478,
"gnomad_exomes_homalt": 68766,
"gnomad_genomes_ac": 41827,
"gnomad_genomes_af": 0.275207,
"gnomad_genomes_homalt": 5962,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 74728,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|Herpes simplex encephalitis, susceptibility to, 1|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.944,
"pos": 186083063,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_003265.3"
}
]
}